Variant report

Variant	rs10941597
Chromosome Location	chr5:42946282-42946283
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:42943601..42947124-chr5:43040849..43043417,3	K562	blood:

Variant related genes	Relation type
ENSG00000215068	Chromatin interaction
ENSG00000177721	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10941595	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11550287	0.88[GIH][hapmap];0.93[MEX][hapmap]
rs11740797	0.90[GIH][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap]
rs11743123	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs11743246	0.80[ASN][1000 genomes]
rs11746790	0.82[EUR][1000 genomes]
rs11747015	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11949444	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11951144	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11954543	0.80[ASN][1000 genomes]
rs11958520	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12153132	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12187928	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12188691	0.85[CHD][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap]
rs13156722	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13173064	0.90[GIH][hapmap];0.86[MEX][hapmap]
rs13177679	0.91[JPT][hapmap]
rs13185118	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2432097	0.85[CEU][hapmap]
rs2548382	0.82[CEU][hapmap]
rs2603626	0.84[EUR][1000 genomes]
rs2603628	0.87[EUR][1000 genomes]
rs2603629	0.87[EUR][1000 genomes]
rs2603649	0.85[CEU][hapmap]
rs309911	0.87[EUR][1000 genomes]
rs309939	0.87[EUR][1000 genomes]
rs309940	0.86[EUR][1000 genomes]
rs316405	0.81[GIH][hapmap]
rs34009007	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34492794	0.80[AMR][1000 genomes]
rs36171678	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3849696	0.85[CEU][hapmap]
rs3849698	0.89[CHD][hapmap];0.95[GIH][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3849699	0.89[CHD][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap]
rs62372095	0.84[EUR][1000 genomes]
rs6889271	0.82[CEU][hapmap]
rs6895732	0.87[EUR][1000 genomes]
rs7709181	0.93[GIH][hapmap];0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
7	nsv1018276	chr5:42809131-42975245	Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv968909	chr5:42903982-42953465	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	esv1806082	chr5:42906572-42967215	Transcr. at gene 5' and 3' Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	esv1813779	chr5:42906572-42992040	Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
11	esv3346992	chr5:42921680-42970055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv1029288	chr5:42928085-43047323	Flanking Bivalent TSS/Enh Active TSS Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	120 gene(s)	inside rSNPs	diseases
13	nsv1020910	chr5:42929799-43000021	Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
14	nsv537738	chr5:42929799-43000021	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
15	nsv528880	chr5:42940230-42967215	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10941597	LOC643977	cis	multi-tissue	Pritchard

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42940400-42948800	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr5:42944600-42948800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:42944600-42948800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:42944600-42948800	Weak transcription	Placenta	Placenta
5	chr5:42944600-42948800	Weak transcription	Spleen	Spleen
6	chr5:42944600-42949800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:42944600-42949800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:42945000-42946400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:42945200-42950000	Weak transcription	HSMMtube	muscle
10	chr5:42945200-42951000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:42945400-42949200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr5:42945400-42949400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:42945600-42948600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr5:42945600-42948800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr5:42945600-42949000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr5:42945600-42949000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:42945600-42949000	Weak transcription	NHLF	lung
18	chr5:42945600-42949200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:42945600-42949400	Weak transcription	HSMM	muscle
20	chr5:42945800-42947800	Weak transcription	A549	lung
21	chr5:42945800-42949000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:42945800-42949000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr5:42945800-42949000	Weak transcription	Hela-S3	cervix
24	chr5:42945800-42949000	Weak transcription	NHDF-Ad	bronchial
25	chr5:42945800-42949000	Weak transcription	Osteobl	bone
26	chr5:42945800-42949200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr5:42945800-42949200	Weak transcription	NH-A	brain
28	chr5:42945800-42949200	Weak transcription	NHEK	skin
29	chr5:42945800-42949400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:42946000-42948800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:42946000-42948800	Weak transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links